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Macellibacteroides Fermentans Gen. Nov., Sp. Nov., a Member of the Family Porphyromonadaceae Isolated from an Upflow Anaerobic Filter Treating Abattoir Wastewaters
International Journal of Systematic and Evolutionary Microbiology (2012), 62, 2522–2527 DOI 10.1099/ijs.0.032508-0 Macellibacteroides fermentans gen. nov., sp. nov., a member of the family Porphyromonadaceae isolated from an upflow anaerobic filter treating abattoir wastewaters Linda Jabari,1,2 Hana Gannoun,2 Jean-Luc Cayol,1 Abdeljabbar Hedi,1 Mitsuo Sakamoto,3 Enevold Falsen,4 Moriya Ohkuma,3 Moktar Hamdi,2 Guy Fauque,1 Bernard Ollivier1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, Case 925, Marie-Laure Fardeau 163 Avenue de Luminy, 13288 Marseille Cedex 9, France [email protected] 2Laboratoire d’Ecologie et de Technologie Microbienne, Institut National des Sciences Applique´es et de Technologie, Centre Urbain Nord, BP 676, 1080 Tunis Cedex, Tunisia 3Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 4CCUG, Culture Collection, Department of Clinical Bacteriology, University of Go¨teborg, 41346 Go¨teborg, Sweden A novel obligately anaerobic, non-spore-forming, rod-shaped mesophilic bacterium, which stained Gram-positive but showed the typical cell wall structure of Gram-negative bacteria, was isolated from an upflow anaerobic filter treating abattoir wastewaters in Tunisia. The strain, designated LIND7HT, grew at 20–45 6C (optimum 35–40 6C) and at pH 5.0–8.5 (optimum pH 6.5–7.5). It did not require NaCl for growth, but was able to grow in the presence of up to 2 % NaCl. Sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and nitrite were not used as terminal electron acceptors. -
Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis Within the Prevalent Canine Oral Species Porphyromonas Cangingivalis
GBE Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis Ciaran O’Flynn1,*, Oliver Deusch1, Aaron E. Darling2, Jonathan A. Eisen3,4,5, Corrin Wallis1,IanJ.Davis1,and Stephen J. Harris1 1 The WALTHAM Centre for Pet Nutrition, Waltham-on-the-Wolds, United Kingdom Downloaded from 2The ithree Institute, University of Technology Sydney, Ultimo, New South Wales, Australia 3Department of Evolution and Ecology, University of California, Davis 4Department of Medical Microbiology and Immunology, University of California, Davis 5UC Davis Genome Center, University of California, Davis http://gbe.oxfordjournals.org/ *Corresponding author: E-mail: ciaran.ofl[email protected]. Accepted: November 6, 2015 Abstract Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and at University of Technology, Sydney on January 17, 2016 plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions char- acterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to syn- thesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. -
Description of Gabonibacter Massiliensis Gen. Nov., Sp. Nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota
Curr Microbiol DOI 10.1007/s00284-016-1137-2 Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota 1,2 1 3,4 Gae¨l Mourembou • Jaishriram Rathored • Jean Bernard Lekana-Douki • 5 1 1 Ange´lique Ndjoyi-Mbiguino • Saber Khelaifia • Catherine Robert • 1 1,6 1 Nicholas Armstrong • Didier Raoult • Pierre-Edouard Fournier Received: 9 June 2016 / Accepted: 8 September 2016 Ó Springer Science+Business Media New York 2016 Abstract The identification of human-associated bacteria Gabonibacter gen. nov. and the new species G. mas- is very important to control infectious diseases. In recent siliensis gen. nov., sp. nov. years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial Keywords Gabonibacter massiliensis Á Taxonogenomics Á species and/or genera. Using this strategy, strain GM7, a Culturomics Á Gabon Á Gut microbiota strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese Abbreviations patient. It is a motile coccobacillus without catalase and CSUR Collection de Souches de l’Unite´ des oxidase activities. The genome of Gabonibacter mas- Rickettsies siliensis is 3,397,022 bp long with 2880 ORFs and a G?C DSM Deutsche Sammlung von content of 42.09 %. Of the predicted genes, 2,819 are Mikroorganismen protein-coding genes, and 61 are RNAs. Strain GM7 differs MALDI-TOF Matrix-assisted laser desorption/ from the closest genera within the family Porphyromon- MS ionization time-of-flight mass adaceae both genotypically and in shape and motility. -
Endosymbiont Diversity and Evolution Across Weevil Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/171181; this version posted August 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Endosymbiont diversity and evolution across weevil tree of life Guanyang Zhang1#, Patrick Browne1,2#, Geng Zhen1#, Andrew Johnston4, Hinsby Cadillo-Quiroz5, and Nico Franz1 1 School of Life Sciences, Arizona State University, Tempe, Arizona, USA 2 Department of Environmental Science, Aarhus University, 4000 Roskilde, Denmark # These authors contributed equally to this work ABSTRACT As early as the time of Paul Buchner, a pioneer of endosymbionts research, it was shown that weevils host diverse bacterial endosymbionts, probably only second to the hemipteran insects. To date, there is no taxonomically broad survey of endosymbionts in weevils, which preclude any systematic understanding of the diversity and evolution of endosymbionts in this large group of insects, which comprise nearly 7% of described diversity of all insects. We gathered the largest known taxonomic sample of weevils representing four families and 17 subfamilies to perform a study of weevil endosymbionts. We found that the diversity of endosymbionts is exceedingly high, with as many as 44 distinct kinds of endosymbionts detected. We recovered an ancient origin of association of Nardonella with weevils, dating back to 124 MYA. We found repeated losses of this endosymbionts, but also cophylogeny with weevils. We also investigated patterns of coexistence and coexclusion. INTRODUCTION Weevils (Insecta: Coleoptera: Curculionoidea) host diverse bacterial endosymbionts. -
Thèses Traditionnelles
UNIVERSITÉ D’AIX-MARSEILLE FACULTÉ DE MÉDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ THÈSE Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 23 Novembre 2017 Par El Hadji SECK Étude de la diversité des procaryotes halophiles du tube digestif par approche de culture Pour obtenir le grade de DOCTORAT d’AIX-MARSEILLE UNIVERSITÉ Spécialité : Pathologie Humaine Membres du Jury de la Thèse : Mr le Professeur Jean-Christophe Lagier Président du jury Mr le Professeur Antoine Andremont Rapporteur Mr le Professeur Raymond Ruimy Rapporteur Mr le Professeur Didier Raoult Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 7278 Directeur : Pr. Didier Raoult 1 Avant-propos : Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Research Article Review Jmb
J. Microbiol. Biotechnol. (2017), 27(0), 1–7 https://doi.org/10.4014/jmb.1707.07027 Research Article Review jmb Methods 20,546 sequences and all the archaeal datasets were normalized to 21,154 sequences by the “sub.sample” Bioinformatics Analysis command. The filtered sequences were classified against The raw read1 and read2 datasets was demultiplexed by the SILVA 16S reference database (Release 119) using a trimming the barcode sequences with no more than 1 naïve Bayesian classifier built in Mothur with an 80% mismatch. Then the sequences with the same ID were confidence score [5]. Sequences passing through all the picked from the remaining read1 and read2 datasets by a filtration were also clustered into OTUs at 6% dissimilarity self-written python script. Bases with average quality score level. Then a “classify.otu” function was utilized to assign lower than 25 over a 25 bases sliding window were the phylogenetic information to each OTU. excluded and sequences which contained any ambiguous base or had a final length shorter than 200 bases were Reference abandoned using Sickle [1]. The paired reads were assembled into contigs and any contigs with an ambiguous 1. Joshi NA, FJ. 2011. Sickle: A sliding-window, adaptive, base, more than 8 homopolymeric bases and fewer than 10 quality-based trimming tool for FastQ files (Version 1.33) bp overlaps were culled. After that, the contigs were [Software]. further trimmed to get rid of the contigs that have more 2. Schloss PD. 2010. The Effects of Alignment Quality, than 1 forward primer mismatch and 2 reverse primer Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies. -
Behavioral Abnormalities of the Gut Microbiota Underlie Alzheimer’S Disease Development and Progression
Journal of Research in Medical and Dental Science 2018, Volume 6, Issue 5, Page No: 246-263 Copyright CC BY-NC 4.0 Available Online at: www.jrmds.in eISSN No. 2347-2367: pISSN No. 2347-2545 The Gut Microbiota-brain Signaling: Behavioral Abnormalities of The Gut Microbiota Underlie Alzheimer’s Disease Development and Progression. Dictatorship or Bidirectional Relationship? Menizibeya O Welcome* Department of Physiology, College of Health Sciences, The Nile University of Nigeria, Nigeria ABSTRACT Over the past decades, renewed research interest revealed crucial role of the gut microbiota in a range of health abnormalities including neurodevelopmental, neurodegenerative and neuropsychiatric diseases such as multiple sclerosis, autism spectrum disorders, and schizophrenia. More recently, emerging studies have shown that dysfunctions in gut microbiota can trigger the development or progression of Alzheimer’s disease (AD), which is the most common neurodegenerative disease worldwide. This paper presents a state-of-the-art review of recent data on the association between dysfunctions of the gut microbiota and AD development and progression. The review stresses on the functional integrity and expression of sealing and leaky junctional complexes of the intestinal and blood-brain barriers as well as contemporary understanding of the multiple mechanisms that underlie the association between barrier dysfunctions and β-amyloid accumulation, resulting to neuro inflammation and subsequently, progressive decrease in cognitive functions. Key determinants of cerebral amyloid accumulation and abnormal gut microbiota are also discussed. Very recent data on the interaction of the gut microbiota and local/distant immunocytes as well as calcium signaling defects that predispose to AD are also discussed. -
Sevasti Filippidou
Sevasti Filippidou University of Neuchatel, 2016 Sporulation Capability and Metabolic Mechanisms of Endospore-Forming Firmicutes under Conditions Limiting for Growth and Survival A dissertation submitted to the University of Neuchatel for the degree of Docteure ès Sciences by Sevasti Filippidou, MSc Molecular Genetics Accepted by the Jury: Prof. Pilar Junier, thesis director, University of Neuchatel Prof. Maarten Voordow, University of Neuchatel Prof. Melanie Blokesch, EPFL, Lausanne Dr. David Russel Johnson, Eawag, Dübendorf Dr. Paul Herron, University of Strathclyde, Glasgow, UK Defended the 11th April 2016 University of Neuchatel Faculté des sciences Secrétariat-décanat de Faculté Rue Emile-Argand 11 2000 Neuchâtel - Suisse Tél: + 41 (0)32 718 2100 E-mail: [email protected] IMPRIMATUR POUR THESE DE DOCTORAT La Faculté des sciences de l'Université de Neuchâtel autorise l'impression de la présente thèse soutenue par Madame Sevasti Filippidou Titre: “Sporulation capability and metabolic mechanisms of endospore-forming Firmicutes under conditions limiting for growth and survival” sur le rapport des membres du jury composé comme suit: - Prof. Pilar Junier, directrice de thèse, Université de Neuchâtel, Suisse - Prof. ass. Maarten Voordouw, Université de Neuchâtel, Suisse - Prof. Melanie Blokesch, EPF Lausanne, Suisse - Dr David R. Johnson, EAWAG, Dübendorf, Suisse - Dr Paul Herron, University of Strathclyde, Glasgow, UK Neuchâtel, le 28 avril 2016 Le Doyen, Prof. B. Colbois Imprimatur pour thèse de doctorat www.unine.ch/sciences This work is dedicated to The memory of Marilena Vourkou, for her inspiration to life, Entropia, that has shaped me to what I am, Dimitris Serafis, without whom I wouldn’t have reached that far. -
Le 23 Novembre 2017 Par Aurélia CAPUTO
AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE T H È S E Présentée et publiquement soutenue à l'IHU – Méditerranée Infection Le 23 novembre 2017 Par Aurélia CAPUTO ANALYSE DU GENOME ET DU PAN-GENOME POUR CLASSIFIER LES BACTERIES EMERGENTES Pour obtenir le grade de Doctorat d’Aix-Marseille Université Mention Biologie - Spécialité Génomique et Bio-informatique Membres du Jury : Professeur Antoine ANDREMONT Rapporteur Professeur Raymond RUIMY Rapporteur Docteur Pierre PONTAROTTI Examinateur Professeur Didier RAOULT Directeur de thèse Unité de recherche sur les maladies infectieuses et tropicales émergentes, UM63, CNRS 7278, IRD 198, Inserm U1095 Avant-propos Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’École Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, les parties introductions et bibliographies sont remplacées par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail. -
Brevibacillus Massiliensis Sp. Nov
Standards in Genomic Sciences (2013) 8:1-14 DOI:10.4056/sigs.3466975 Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Perrine Hugon1†, Ajay Kumar Mishra1†, Jean-Christophe Lagier1, Thi Thien Nguyen1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1* 1Aix-Marseille Université, URMITE, Faculté de médecine, France † These two authors have equal contribution * Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Brevibacillus massiliensis, genome, culturomics, taxono-genomics Brevibacillus massiliensis strain phRT sp. nov. is the type strain of B. massiliensis sp. nov., a new species within the genus Brevibacillus. This strain was isolated from the fecal flora of a woman suffering from morbid obesity. B. massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%. Introduction Brevibacillus massiliensis strain phRT (= CSUR brevis and B. centrosporus were isolated from in- P177 = DSM 25447) is the type strain of B. door dust in schools, day care centers for children massiliensis sp. nov. This bacterium is a Gram- and animal sheds [26], and fecal flora of children, positive, spore-forming, indole negative, aerobic respectively [27]. However, several Brevibacillus and motile bacillus that was isolated from the species are also frequently isolated from humans, stool of a 26-year-old woman suffering from mor- notably in nosocomial infections, causing breast bid obesity. -
Noncontiguous Finished Genome Sequence And
NEW MICROBES IN HUMANS Noncontiguous finished genome E-mail: [email protected] sequence and description of Paenibacillus antibioticophila T sp. nov. GD11 , the type strain Introduction of Paenibacillus antibioticophila Paenibacillus antibioticophila strain GD11T (= DSM 28228 = CSUR P1358) is the type strain of Paenibacillus antibioticophila 1,2 1 1 1,2 G. Dubourg , T. Cimmino , S. a. Senkar , J.-C. Lagier , sp. nov. It is a Gram-positive, aerobic, indole-negative rod- 1 1 3 1,2,4 C. Robert , C. Flaudrops , P. Brouqui , D. Raoult , shaped bacterium isolated as part of a culturomics study [1,2]. 1,2 1,2 P.-E. Fournier and J.-M. Rolain This bacterium was isolated from a 63-year-old woman with 1) Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, multidrug-resistant tuberculosis who was receiving a broad- UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire spectrum antibiotic regimen at the time of stool collection, as Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 2) Pôle recently reported [2]. des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de The current classification of prokaryotes is based on a com- Bactériologie–Hygiène–Virologie, University, Hospital Centre Timone, Institut bination of phenotypic and genotypic characteristics [3,4] which Hospitalo-Universitaire (IHU) Méditerranée Infection, 3) Service des Maladies includes 16S rRNA gene phylogeny, G+C content and DNA– Infectieuses et Tropicales. Hôpital Nord, Assistance Publique-Hôpitaux de DNA hybridization. Although these tools are considered to be Marseille, France and 4) Special Infectious Agents Unit, King Fahd Medical the reference standard, they have several pitfalls [5,6]. -
Templat Tesis Dan Disertasi
BACTERIAL DIVERSITY AND LIPASE PRODUCING BACTERIA IN FOREST AND OIL PALM PLANTATION AT SAROLANGUN JAMBI INDONESIA MARINI WIJAYANTI GRADUATE SCHOOL BOGOR AGRICULTURAL UNIVERSITY BOGOR 2015 DECLARATION OF THE SOURCE OF THIS DISSERTATION I declare that this dissertation, entitled Bacterial Diversity and Lipase Producing Bacteria in Forest and Oil Palm Plantation at Sarolangun Jambi Indonesia is entirely my own work, assisted by a supervisory committee and has not been submitted in any form for another degree or diploma to any university or other tertiary institution of education. Where this dissertation draws on existing publications, those sources are cited in the text and listed in the references section. Bogor, August 2015 Marini Wijayanti G361110011 RINGKASAN MARINI WIJAYANTI. Keragaman Bakteri dan Bakteri Penghasil Lipase dalam Hutan dan Perkebunan Sawit di Sarolangun Jambi Indonesia. Dibimbing oleh ANJA MERYANDINI, ARIS TRI WAHYUDI, and MUNTI YUHANA. Deforestasi untuk pembukaan lahan perkebunan sawit paling masif terjadi di Asia Tenggara. Hal ini berdampak negatif pada keragaman hayati dan lingkungan. Tanah dan sedimen pada penelitian ini diperoleh dari lapisan atas tanah hutan dataran rendah dan perkebunan sawit, serta perairan yang disekitar situs tersebut. Hutan tersebut berlokasi di Taman Nasional Bukit Duabelas, dan perkebunan sawit sekitar hutan di Sarolangun Jambi Indonesia. Keragaman komunitas bakteri dari tanah dan sedimen perairan area hutan dan kebun sawit Sumatra dipelajari menggunakan pyrosequencing gen 16S rRNA dan indeks keragaman umumnya. Pendekatan filogenetik digunakan untuk mengungkap perubahan komunitas filotipe bakteri dan genusnya di kedua area. Pendekatan ekologis menggunakan nilai pH, kandungan Karbon (C) total, Nitrogen (N) total, Fosfor (P) tersedia dan keragaman bakteri menggunakan indeks Shannon dan Simpson, dan kelimpahan bakteri dengan indeks Chao1-ACE dan OTUs.